[Sean Simms]"I outputted in a variety of formats and with a variety of destinations (dvd and youtube)
but all showed the same problems.
"

I forget which version of compressor you have - v2 or v3? I feel like it's 3.

There are a couple of 'general' workarounds you might try before we have to play with nuts and bolts.
Try doing an export to QuickTime (via QuickTime movie, not QuickTime convert); then feed that to compressor.
Or if that's what you're doing now, try a direct export to compressor.

Don't send the whole show - just a 30 sec sample of the compressed area.

If you built your own compressor settings (like I'm guessing for youtube), try really torquing out the data rate, Double it and see if you have the same problem. Triple it if you have to.